Contacts of the helix formed by residues 336 - 349 (chain A) in PDB entry 6B0O
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 336 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323A PHE* 3.5 8.2 - - - -
334A TYR* 3.8 6.4 - - - +
335A PHE* 1.3 87.3 - - + +
337A LEU* 1.3 64.1 + - - +
338A SER* 3.9 17.5 - - - +
339A HIS* 3.3 44.3 + - + +
340A LEU 3.3 8.7 + - - -
11B T 6.1 0.7 - - - -
12B G 5.1 10.6 + - - -
13B T 3.6 30.5 + - - +
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Residues in contact with LEU 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A PHE* 3.5 40.9 - - + -
336A LYS* 1.3 71.8 - - - +
338A SER* 1.3 57.3 + - - +
340A LEU* 3.2 13.6 + - + +
341A GLN* 2.8 65.3 + - + +
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Residues in contact with SER 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A LYS* 3.9 15.8 - - - +
337A LEU* 1.3 79.8 - - - +
339A HIS* 1.3 67.5 + - - +
341A GLN* 3.8 13.9 + - - +
342A MET* 2.9 30.5 + - - +
1C T 3.6 31.6 + - - +
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Residues in contact with HIS 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A TYR* 3.7 23.5 - + + +
335A PHE* 5.0 2.4 + - + +
336A LYS* 3.3 45.3 + - + +
337A LEU 3.2 0.6 - - - -
338A SER* 1.3 88.0 + - - +
340A LEU* 1.3 56.7 + - - +
342A MET* 3.4 6.5 + - + +
343A HIS* 2.9 30.0 + - - +
11B T 3.5 66.2 + + + +
12B G 5.1 7.1 + - - -
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Residues in contact with LEU 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A PHE* 3.7 31.9 - - + +
324A MET 3.7 17.0 - - - +
325A CYS* 3.7 37.2 - - + +
334A TYR* 3.7 21.9 - - + -
336A LYS 3.3 2.6 + - - -
337A LEU* 3.2 19.1 + - + +
339A HIS* 1.3 75.3 - - - +
341A GLN* 1.3 61.8 + - + +
343A HIS* 3.2 3.6 + - + +
344A SER* 2.9 39.2 + - - +
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Residues in contact with GLN 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A LEU* 2.8 55.7 + - + +
338A SER* 3.8 15.0 - - - +
340A LEU* 1.3 73.1 - - + +
342A MET* 1.3 63.1 + - - +
344A SER* 3.4 18.6 + - - -
345A ARG* 3.7 12.1 + - - +
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Residues in contact with MET 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A SER 2.9 18.0 + - - +
339A HIS* 3.7 6.7 - - + +
341A GLN* 1.3 74.4 - - - +
343A HIS* 1.3 64.6 + - - +
345A ARG* 3.1 52.5 + - - +
346A LYS 4.2 1.0 + - - -
353A TYR* 5.6 1.6 - - + +
365A SER* 3.2 27.7 - - - +
366A ARG* 3.6 32.3 - - + -
1C T 6.6 0.2 - - - +
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Residues in contact with HIS 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A CYS* 3.9 16.4 - - + -
330A CYS* 3.4 4.6 - - - -
332A LYS* 3.7 23.9 + - + +
334A TYR* 3.1 34.0 + + + +
339A HIS 2.9 17.3 + - - +
340A LEU* 3.6 5.8 - - + +
342A MET* 1.3 76.0 - - - +
344A SER* 1.3 59.9 + - - +
346A LYS* 2.9 47.8 + - + +
347A HIS* 3.3 7.4 + + - -
504A ZN 2.1 35.8 - - - -
10B G 4.7 3.9 + - - +
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Residues in contact with SER 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A CYS* 5.2 3.8 - - - -
340A LEU* 2.9 31.2 + - - +
341A GLN* 3.6 10.9 - - - -
342A MET 3.2 0.4 - - - -
343A HIS* 1.3 80.4 - - - +
345A ARG* 1.3 60.1 + - - +
347A HIS* 3.2 21.5 + - - +
348A THR* 3.3 19.3 + - - +
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Residues in contact with ARG 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A GLN 3.9 10.5 + - - +
342A MET* 3.4 38.2 - - - +
343A HIS 3.0 1.2 + - - -
344A SER* 1.3 75.0 - - - +
346A LYS* 1.3 55.7 + - - +
347A HIS 3.3 0.2 - - - -
348A THR* 3.4 7.9 - - - -
349A GLY* 2.7 30.1 + - - -
350A GLU* 3.3 53.5 + - - +
351A LYS* 6.0 0.5 - - - -
352A PRO* 3.9 21.0 - - - +
353A TYR* 4.1 8.7 + - - -
365A SER* 2.9 33.5 + - - +
1C T 5.0 9.3 - - - -
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Residues in contact with LYS 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A CYS* 6.3 0.4 - - - -
332A LYS* 4.8 12.5 - - - +
342A MET 4.2 1.0 + - - -
343A HIS* 2.9 34.5 + - + +
345A ARG* 1.3 79.0 - - - +
347A HIS* 1.3 71.3 + - + +
349A GLY* 3.8 6.3 + - - -
365A SER* 5.7 0.9 - - - -
9B A 3.4 33.3 + - - +
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Residues in contact with HIS 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A CYS* 3.8 4.9 - - - -
327A TYR* 3.4 65.7 + + + +
330A CYS* 4.0 9.2 - - + -
343A HIS* 3.3 9.7 + + - -
344A SER* 3.2 16.9 + - - +
346A LYS* 1.3 90.2 + - + +
348A THR* 1.3 65.0 + - + +
504A ZN 2.1 37.7 - - - -
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Residues in contact with THR 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A SER* 3.3 14.1 + - - +
345A ARG* 3.3 13.0 + - - -
347A HIS* 1.3 80.8 - - + +
349A GLY* 1.3 62.8 + - - +
350A GLU* 3.3 20.5 + - - +
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Residues in contact with GLY 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A ARG 2.7 16.4 + - - -
346A LYS 3.8 5.5 + - - -
347A HIS 3.5 2.8 - - - -
348A THR* 1.3 72.6 - - - +
350A GLU* 1.3 61.4 + - - -
351A LYS* 3.2 21.0 + - - +
363A ARG* 5.0 7.8 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il